Antigen Tracking Figures
Ryan Sheridan
2024-04-03
Figure 1
Antigen persists in discrete cell populations within the lymph node
- Experimental design
- UMAP projections show LEC and DC subsets
- Antigen signal is shown for LEC subsets for each time point
- Antigen signal is shown for DC subsets for each time point
Figure 2
Identification of an antigen archiving gene signature
- Ag-scores are shown for dat 14 Ag-high and Ag-low cells
- The top 3 gene ontology terms are shown for Ag-high gene modules
- The expression of each Ag-high gene module is shown for naive LECs (day 0) along with each immunization time point.
Figure 3
Predicting antigen archiving ability
- The fraction of cells predicted to be Ag-competent is shown for LECs
- F1 scores are shown for random forest models trained using day 14 LECs
- Ag-high module scores are shown for predicted Ag-competent LECs
- Select example genes from the cLEC Ag-high gene module are shown, triangles indicate the gene is upregulated when compared to Ag-low
Figure 4
Antigen archiving is enhanced by sequential vaccinations
- Experimental design
- Ag-score is shown for single and dual vaccinations for the 21 day timepoint for each LEC subset. Other timepoints are shown in grey. P values were calculated using a one-sided Wilcoxon rank sum test with Benjamini-Hochberg correction.
- Successive vaccinations enhances retention of previously archived antigen. Ag-score is shown for the 42 day timepoint as described in C.
- Ag-high module scores described in Figure 2 are shown for LECs that archived antigens from both vaccinations (double-high), from only one vaccination (single-high), or have low levels of both antigens (Ag-low). Module scores are shown for the corresponding LEC subset. P values were calculated using a one-sided Wilcoxon rank sum test with Benjamini-Hochberg correction.
Figure 5
Antigen exchange with DCs correlates with levels of antigen archiving
- Annotated regions, segment types, and antigen signal is shown for a representative lymph node analyzed using the GeoMx DSP platform
- Relative antigen signal is shown for each region segmented based on Lyve1 (LECs) and CD11C (DCs)
- Antigen signal is shown for regions that included both Lyve1+ and CD11C+ segments
Figure 6
Antigen archiving is impaired during CHIKV infection
- The fraction of predicted Ag-competent cLECs is shown for mock and CHIKV-infected mice
- cLEC Ag-high module scores are shown for mock and CHIKV-infected mice
- The percentage of ova+ LECs for mice infected with WT CHIKV or an attenuated strain (CHIKV 181/25)
Session info
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
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## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
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## time zone: America/Denver
## tzcode source: system (glibc)
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## attached base packages:
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## other attached packages:
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